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Bibutils configuration

2005-05-02
2013-05-28
  • Hi,

    i did not install the scripts using install.php file.

    Where can i change (manually) the path to the bibutils directory?

    Thanks,

    Andsilva

     
    • Hi  Andsilva,

      assuming your literature database is named 'literature' and your path to bibutils is '/usr/local/bin/', issue the following command from your MySQL command line interpreter:

      UPDATE literature.depends SET depends_path = '/usr/local/bin/', depends_enabled = 'true' WHERE depends_external = "bibutils";

      Note that the path spec must end with a slash.

      HTH, Matthias

       
    • Thanks Matthias

      Up and Runing : )

       
    • Hi, I do like Andsilva but it doesn't work !!! when i try to import I have those two error :

      There were validation errors regarding the data you entered:

      and

      Source data missing!

      (I have tried to import a db coming from RefManager 11 :-(

      I Work on a sme-server7 (linux based on centos) and i follow the tutorial for installing bibutils ... and it doesn't work ... pls help me

      Achel_Jay
      acheljay2@hotmail.com

       
      • This does not sound like a bibutils problem.

        Can you successfully import records that don't require bibutils?  Try pasting the text from:
        http://wiki.refbase.net/index.php/Import_Example:_CSA
        into the record text box & also try putting it into a file & importing that file.

        If that works, try the example files on the refbase wiki for whatever format you're using in RefManager.

        --Rick

         
        • It works fine when I make a copy and paste into the import textbox but it don't work when i try to import it in a .txt file ...

          I check my php.ini and all the options are "on" ... I don't understand why it doesn't work ... chmod problem on bibutils ??? function of upload ???

           
          • Hi,

            > It works fine when I make a copy and paste into the import textbox
            > but it don't work when i try to import it in a .txt file ...

            Which format(s) are you trying to import?

            If you've tried to import Endnote Refer data, have you also tried other formats, such as RIS? Is the results always the same? (i.e. import via text box works, but file upload doesn't)

            And are you able to upload & attach PDF files to existing records? Or do these file uploads fail as well?

            Does export to Endnote/RIS/BibTeX work as expected? (this would indicate that Bibutils is working correctly)

            And is safe_mode enabled on your PHP server?

            Thanks, Matthias

             
            • Hi, I try all the format (RIS, TXT, XML, ...) of refmanager : it works on the test server but not on my server ... for the export => I delete all the prépost data ... so, i can't test it.

               
              • We think that you are having a problem uploading files to your server, but we need you to carefully test this & respond to us with the results.  This will help us to confirm the problem is what we think that it is & will allow us to help you to fix it.  Please try the following:

                (1) Create a new record either manually or by using the text box.
                (2) Edit the record and attempt to attach a file.  Please respond with whether or not this works.
                (3) Attempt to export the record to bibtex.  Please respond with whether of not this works.

                Thanks,

                Rick

                 
    • Hi,

      seems like I've the same problem. I installed refbase via install.php. The path to bibutils (version 3.41) is usr/local/bin/ like U suggested and the install script detected. The folder and the files are executable for the root user. However refbase is running under another user (web0) so I tried to install bibutils under another path wich is executable for web0 and changed the path in the depends table.

      Anyhow the import problems stay the same... I tried with both my own data and the example records in the wiki.

      Import via import.php trough import form and file upload:

      Endnote - There were validation errors regarding the data you entered:
      Reference Manager (RIS) - works!
      BibTeX - There were validation errors regarding the data you entered:
      RefWorks - works!
      SciFinder - There were validation errors regarding the data you entered: Unrecognized data format!
      PubMed MEDLINE - There were validation errors regarding the data you entered:
      PubMed XML - There were validation errors regarding the data you entered:
      ISI Web of Science - There were validation errors regarding the data you entered: Unrecognized data format!
      MODS XML - There were validation errors regarding the data you entered:

      Export:
      BibTeX - empty file
      Endnote - empty file
      RIS - empty file
      MODS XML - works!
      ODF XML - seems to work

      Other conf.: safe_mode is off / root has no access to my literature database!!

      Thanks!

       
    • Hi Carsten,

      sorry that the refbase/Bibutils integration is causing you so much trouble!

      Are you using refbase-0.9.0 or a newer version from the refbase SVN repository? Which server platform and Apache/PHP/MySQL versions are you using?

      And where did you install your refbase scripts: locally (under XAMPP?) or on a remote server? If the latter, is this server fully accessible to you or is it on a shared host?

      If you've installed refbase locally and haven't used XAMPP (xampp.org), it might be worth trying, since it may potentially avoid other problems with your current server setup.

      Also, please see the the section "Export of records results in a blank page" at our installation troubleshooting page:

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

      Please make sure that the path to the Bibutils programs given in table depends ends with a slash.

      W.r.t. the permission settings, the permissions for Bibutils must be set so that the Bibutils programs can be executed by your web server (Apache/PHP).

      Also, what's your server's PHP temporary/session directory? refbase & Bibutils read/write files from/to this directory, so this directory must be accessible & writable by Apache/PHP/Bibutils. refbase-0.9.0 uses the PHP function 'session_save_path()' to determine the PHP temp/session directory. However, if you're on a shared host, the temp directory may need to be hardcoded into file 'includes/execute.inc.php' (line 154). In case of the SVN versions (> refbase-0.9.0), there's a variable ('$sessionTempDir') in 'initialize/ini.in.php' to explicitly set the PHP temp/session directory.

      If you can, it's also worth checking that you can run Bibutils manually from the command line, and have it successfully write data to the servers PHP temporary/session directory.

      Import of Endote, BibTeX, PubMed XML, Copac and MODS XML requires Bibutils so these formats are not expected to work until Bibutils has been setup correctly for use with refbase.

      http://bibutils.refbase.net/

      However, you report that you also weren't able to import records from SciFinder, PubMed MEDLINE and ISI Web of Science? This is strange, since these import formats do not require Bibutils but are supported natively by refbase -- so they should work even without Bibutils being installed. Could you post some sample records? And have you tried to import the exact same records into the refbase demo database (http://demo.refbase.net/)? Do they import fine there?

      I've heard issues from some users that line endings could cause problems when using the file upload feature of the import form. Have you tried to copy & paste the same SciFinder/MEDLINE/ISI records into the import form? Does this work better?

      I hope that we'll be able to resolve your issues.

      Best, Matthias

       
    • Hi,

      first of all thank you for your quick respond. I've solved the problem with bibutils. When I said that I've "installed" bibutils, I ment that I've copied the files into usr/local/bin/. That doesn't work.

      Ok, so what else have I done? I copied the C source code file "bibutils_3.41_src.tgz" to a directory executable for root and unzipped it. After that I changed into that directory and commanded "./configure" than "make" and "make install", so it compiled the files for my system and installed them into usr/local/bin/.

      I've no idea if this is the usual way to install bibutils, but it works for me.

      Thanks a lot!

      Carsten

       
    • Hi Carsten,

      I'm glad that Bibutils is working for you now!

      > I've no idea if this is the usual way to install bibutils

      If one wants to install Bibutils for Windows, x86 Linux or Mac OS X, one would normally just download the Bibutils binaries from:

      http://www.scripps.edu/~cdputnam/software/bibutils/

      and copy them to an executable path (making sure that permissions are set correctly so that the server can execute them).

      If one needs to install Bibutils on any other platform (such as Sun OS), then one would generally need to compile it from source.

      If Bibutils gets installed to a common path (such as 'usr/local/bin/') or if the Bibutils path can be symlinked into the main refbase directory, then things should usually work fine. But, as mentioned above, depending on the individual server setup, there can be issues with permissions and/or the PHP temporary/session directory (especially for shared hosts).

      Best regards, Matthias

       
    • marcio_tex
      marcio_tex
      2008-11-11

      Hi.

      I had same problem. Compiles works because my host arch is x86_64 (dreamhost) and linux binaries are compile for 32. So, I repite one Matthias point: test if bibutil binarie run correctly into server.

      Best regards,

       
    • Enro
      Enro
      2009-04-02

      I also seem to experience trouble with Refbase + Bibutils. Everything works for me (file upload, CSA or MEDLINE import, MODS XML export) except options that necessitate Bibutils.

      I have changed the Bibutils path in the SQL table to /home/www/enro/cgi-bin/ (the absolute path to the corresponding folder on my mutualized web host). I have checked the chmod to the Bibutils folder. The only thing which I cannot figure out is whether I should customize the $sessionTempDir variable (but I noticed that Refbase breaks down when I try to guess it so it is probably best to leave it as is).

      I don't really know what I am missing here. As I am on a mutualized web host there is not so much I can do to try run Bibutils with command line and so on. One thing that you should know, though, is that I have created the cgi-bin folder myself (as advised by the helpdesk of me host) and am trying to use it for the first time...

      Any help would be highly appreciated. Thank you!

      Antoine

       
    • Hi Antoine,

      which version of Bibutils are you using? There have been reports[*] from other users about problems with Bibutils v4.1, while Bibutils v3.4 seems to be working fine.

      [*]: see e.g. here: https://sourceforge.net/forum/forum.php?thread_id=3098699&forum_id=218758

      If you haven't done so, try getting Bibutils 3.40 from the refbase Bibutils mirror and see whether that works better:

      http://bibutils.refbase.org/

      Also, does your server run in PHP 'safe_mode'? In that case, the Bibutils programs must be installed in the directory that's specified in the 'safe_mode_exec_dir' setting. And if the PHP 'exec' command is somehow blocked on your server, the call to Bibutils won't work. A call to 'phpinfo()' and/or your server's friendly help desk person might give you answers to these questions.

      Matthias

       
    • Enro
      Enro
      2009-04-03

      Thank you fo the hints. I have reinstalled Bibutils v. 3.40, applying the right chmod each time and also trying different versions (OS X, Win, i386) as I wasn't sure of the system of my mutualized server. It didn't make a difference.

      Now :

      - "safe_mode" is off on my host
      - but "exec" is mentioned on the "disable_functions" line.

      Does it mean my host would not allow me to run these scripts? In which case I probably should check with them...

      Thank you,

      Antoine

       
    • Hi Antoine,

      > - but "exec" is mentioned on the "disable_functions" line.
      >
      > Does it mean my host would not allow me to run these scripts?

      I fear so, yes. Many ISPs disable the PHP exec command due to security considerations.

      > In which case I probably should check with them...

      Yes. They might be able to offer you a solution.

      Best, Matthias

       
    • Enro
      Enro
      2009-04-03

      It turns out I was able to change the settings for exec() myself. I also did it for shell_exec() to be safe... But nothing changes.

      If it helps, here is the configuration of my web host:

      Linux 2.4.20-28.9
      Apache 2.2.8 (Unix)
      MySQL 4.0.26
      PHP 4.4.8

      Well, let me know if you are running out of ideas and I will move on to something else! :-(

      Thank you again for the help,

      Antoine

       
    • Hi Antoine,

      > I was able to change the settings for exec() myself. I also
      > did it for shell_exec() to be safe... But nothing changes.

      I find it a bit surprising that your ISP allows you to change that setting yourself. I'd contact them to make sure that you're really allowed to execute shell tools from PHP scripts now.

      Also please ask the people at your ISP help desk about the exact (full) path to your PHP session/temp directory. This must be specified for variable '$sessionTempDir' (in file 'initialize/ini.inc.php').

      HTH, Matthias

       
      • Enro
        Enro
        2009-04-04

        I have asked the questions that you suggested, let's wait for the answers now...

        Also, I have tried to change the value of '$sessionTempDir' to "/home/www/enro/sessions" (full path to the folder that contains the PHP sessions created by my site, as my ISP explained) but then I get a blank page from Refbase..

        Antoine

         
    • Hi Antoine,

      > Also, I have tried to change the value of '$sessionTempDir' to
      > "/home/www/enro/sessions" (full path to the folder that contains the
      > PHP sessions created by my site, as my ISP explained) but then I get
      > a blank page from Refbase..

      Just so that I understand you correctly: are you saying that when you are using:

      $sessionTempDir = "/home/www/enro/sessions";

      you always get a blank page (no matter what refbase page you're trying to access)?

      Or do you just a get blank page when trying to impot/export any of the formats that require Bibutils?

      I assume the latter?

      Upon import/export, refbase needs to pass its source data to Bibutils for conversion. To do so, refbase (as well as the Bibutils programs) need to be able to read from (and write to) the PHP temp/session directory. If you have access to that directory, you can check whether these temp files actually get created. The names of the temp files created by refbase start with "refbase-".

      in your case, refbase and/or Bibutils don't seem to be able to write to (or read from) that temp/session directory. As a result, you're getting a blank page. Also, if Bibutils isn't allowed to execute, it obviously cannot write to the temp directory.

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

      Matthias

       
      • Enro
        Enro
        2009-04-10

        Thank you very much, this is fixed now.

        The first problem was with the temp directory. Basically, I had forgotten to leave the ";" at the end of the line and your message reminded me to! FYI, you could modifiy the comment line in the ini.inc.php file to read more clearly:

        // e.g. session_save_path(); or "/var/www/web12345/phptmp";

        Then, it appeared that the Bibutils version I had installed was not correct for the system of my webhost. They exceptionally accepted to recompile it and everything is in order now! I'm so glad :-)

        Thank you very much for our help and the tremendous work on Refbase!!

        Antoine

         
      • LaurieF
        LaurieF
        2009-05-15

        Hi

        A fantastic program - thanks for the great work

        My experience with bibutils installation - I tried all the suggestions to get bibutils 4.1 to work ... to no avail :(

        But...works beautifully after compiling from source for my fedora 5 (I know its old :) ) ...without having to change any of the defaults in inc.inc.php  :)

        Compiling was easy - It has been set up well with easy follow instructions ....even for a first time compiler like myself

        Thanks again  :)